flowGraph-class {flowGraph}R Documentation

'flowGraph': A class for storing cell count feature values for the Phenotype class.

Description

'flowGraph': A class for storing cell count feature values for the Phenotype class.

Usage

## S4 method for signature 'flowGraph'
show(object)

Arguments

object

A flowGraph object.

Value

a flowGraph object.

Methods (by generic)

Slots

feat

A list containing elements node and edge, each containing a list with feature values; each element in this list is named by the feature name and contains a numeric matrix with the sample id's as row names and cell populations phenotype labels or edge labels as column names. Column names for edge features are labelled as <from>_<to> e.g. A+_A+B+.

feat_desc

A list containing elements node and edge, each containing a data frame describing the features in the feat slot with columns:

summary

A list containing elements node and edge, each containing a list with a feature summary list; each feature summary in this list contains elements:

summary_desc

A list containing elements node and edge, each containing a data frame describing the features in feat with columns:

meta

A data frame containing the column(s) id (sample id's corresponding to row names of features in the feat slot) and any other meta data pertaining to samples being analyzed.

markers

A character vector containing markers used.

edge_list

A list containing elements child and parent. These elements contain an edge list from child to parent and vice versa.

graph

A list containing data frames v and e with information on cell population nodes and edges. v contains columns:

plot_layout

A string indicating the name of the igraph layout function used to layout the cell population nodes for plotting.

etc

A list containing other information (see fg_get_summary for other things stored in this slot):

Creating Objects

Objects can be created using new("flowFrame") or the constructor flowGraph, with mandatory argument input_. Creating objects using new is discouraged.

Methods

'object' represents a flowGraph object.

Examples


 showClass("flowGraph")

[Package flowGraph version 1.0.0 Index]